SAXSdb — 9meh

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1. 结构基本信息 1. Structure Basics

条目编号 entry_id	9meh
沉积日期 deposition_date	2024-12-06
结构标题 title	Crystal structure of the dimodular LgrA after protein ligation
关键词 keywords	NRPS, Condensation, Dimodule, Complex, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
实验方法 method	X-RAY DIFFRACTION

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2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	45.55 Å
回转半径 Rg (电子) rg_electron	45.23 Å
零角强度 I(0) i0	592232000.00
分子量 molecular_weight	204680.0 kDa
排除体积 excluded_volume	257760 Å³
包络体积 envelope_volume	349380 Å³
水化壳体积 shell_volume	65141 Å³
包络直径 envelope_diameter	199.1 Å
壳层 Rg shell_rg	48.94 Å
包络 Rg envelope_rg	45.46 Å
形状 Rg shape_rg	45.25 Å
总 Rg total_rg	45.32 Å
总原子数 total_atoms	14432
残基数 n_residues	1811
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	180.9 Å
Rg (实空间) rg_real	45.56 Å
Rg 误差 (实空间) rg_real_error	2.35 Å
I(0) (实空间) i0_real	5.9220e+08
I(0) 误差 (实空间) i0_real_error	1.2230e+07
Rg (倒空间) rg_reciprocal	45.55 Å
I(0) (倒空间) i0_reciprocal	592200000.0000
解质量估计 total_estimate	0.7974
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	62.0 Å
偏度 Skewness skewness	0.322
峰度 Kurtosis kurtosis	-0.085
角度范围 angular_range	— – 0.1750 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	89880000.0000
实空间数据点数 n_real_points	36
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.546; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.791; Smooth: 0.932

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4. 晶体学与实验 4. Crystallography & Experiment

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5. 实体与聚合体信息 (2)

Entity 1 polymer

描述 description	Linear gramicidin synthase subunit A
分子量 formula_weight	206064.3 kDa
来源方法 src_method	man
拷贝数 entity_count	1

聚合体 Polymer

聚合体类型 type	polypeptide(L)
链编号 strand_id	A
原子数 atom_count	14432

SAMGRILFLTTFMSKGNKVVRYLESLHHEVVICQEKVHAQSANLQEIDWIVSYAYGYILDKEIVSRFRGRIINLHPSLLPWNKGRDPVFWSVWDETPKGVTIHLIDEHVDTGDILVQEEIAFADEDTLLDCYNKANQAIEELFIREWENIVHGRIAPYRQTAGGTLHFKADRDFYKNLNMTTVRELLALKRLCAEPKRGEKPIDKTFHQLFEQQVEMTPDHVAVVDRGQSLTYKQLNERANQLAHHLRGKGVKPDDQVAIMLDKSLDMIVSILAVMKAGGAYVPIDPDYPGERIAYMLADSSAAILLTNALHEEKANGACDIIDVHDPDSYSENTNNLPHVNRPDDLVYVMYTSGSTGLAKGVMIEHHNLVNFCEWYRPYFGVTPADKALVYSSFSFDGSALDIFTHLLAGAALHIVPSERKYDLDALNDYCNQEGITISYLPTGAAEQFMQMDNQSFRVVITGGDVLKKIERNGTYKLYNGYGPTECTIMVTMFEVDKPYANIPIGKPIDRTRILILDEALALQPIGVAGELFIVGEGLGRGYLNRPELTAEKFIVHPQTGERMYRTGDRARFLPDGNIEFLGRLDNLVKIRGYRIEPGEIEPFLMNHPLIELTTVLAKEQADGRKYLVGYYVAPEEIPHGELREWLGNDLPDYMIPTYFVHMKAFPLTANGKVDRRALPDVQADAELLGEDYVAPTDELEQQLAQVWSHVLGIPQMGIDDHFLERGGDSIKVMQLIHQLKNIGLSLRYDQLFTHPTIRQLKRLLTEQKQVNGLLEPLRELDEQAEYETSAVEKRMYIIQQQDVESIAYNVVYTINFPLTVDTEQIRVALEQLVLRHEGLRSTYHMRGDEIVKRIVPRAELSFVRQTGEEESVQSLLAEQIKPFDLAKAPLLRAGVIETADKKVLWFDSHHILLDGLSKSILARELQALLGQQVLSPVEKTYKSFARWQNEWFASDEYEQQIAYWKTLLQGELPAVQLPTKKRPPQLTFDGAIQMYRVNPEITRKLKATAAKHDLTLYMLMLTIVSIWLSKMNSDSNQVILGTVTDGRQHPDTRELLGMFVNTLPLLLSIDHEESFLHNLQQVKAKLLPALQNQYVPFDKILEAARVKREGNRHPLFDVMFMMQGAPETELESNMHHINAGISKFDLTLEVLERENGLNIVFEYNTHLFDEGMILRMVAQFEHLLLQAVHGLDQQVKRFELVTEDEKRDLFLRVNDTAKAYPNKLIMSMLEDWAAATPDKTALVFREQRVTYRELNERVNQLAHTLREKGVQPDDLVMLMAERSVEMMVAIFAVLKAGGAYLPIDPHSPAERIAYIFADSGAKLVLAQSPFVEKASMAEVVLDLNSASSYAADTSNPPLVNQPGDLVYVMYTSGSTGKPKGVMIEHGALLNVLHGMQDEYPLLQDDAFLLKTTYIFDISVAEIFGWVPGRGKLVILEPEAEKNPKAIWQAVVGAGITHINFVPSMLIPFVEYLEGRTEANRLRYILACGEAMPDELVPKVYEVLPEVKLENIYGPTEATIYASRYSLAKGSQESPVPIGKPLPNYRMYIINRHGQLQPIGVPGELCIAGASLARGYLNNPALTEEKFTPHPLEKGERIYRTGDLARYREDGNIEYLGRMDHQVKIRGYRIELDEIRSKLIQEETIQDAVVVARNDQNGQAYLCAYLLSEQEWTVGQLRELLRRELPEYMIPAHFVLLKQFPLTANGKLDRKALPEPDGSVKAEAEYAAPRTELEATLAHIWGEVLGIERIGIRDNFFELGGDSIKGLQIASRLQRINWTMVINHLFLYPTIEQIAPFVTSEQVVIEAAAENLYFQ

来源 Source

来源生物 organism	Brevibacillus parabrevis
NCBI 分类编号 ncbi_taxonomy_id	54914
宿主生物 host_organism	Escherichia coli

Entity 2 non-polymer

描述 description	[(3~{R})-4-azanyl-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate
分子量 formula_weight	227.2 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 引用文献 (1)

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晶胞边长 a length_a	119.235 Å
晶胞边长 b length_b	166.281 Å
晶胞边长 c length_c	178.491 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	4

空间群 space_group	P 21 21 21
空间群编号 int_tables_number	19
晶系 crystal_system	orthorhombic

分辨率 resolution	3.600 Å
最低分辨率 resolution_low	48.380 Å
R 因子 r_factor	0.2672
R_work r_work	0.2669
R_free r_free	0.2734

fit	/app/data/saxs_computation/me/9meh/9meh.fit
pddf	/app/data/pr_computation/me/9meh/9meh.pr.out
profile	/app/data/saxs_computation/me/9meh/9meh.dat

Crystal structure of the dimodular LgrA after protein ligation

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

1. 结构基本信息 1. Structure Basics

2. SAXS 参数 (CRYSOL 理论计算) 2. SAXS Parameters (CRYSOL)

3. P(r) 距离分布 (GNOM 反演) 3. P(r) Analysis (GNOM)

4. 晶体学与实验 4. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

衍射实验 Diffraction

5. 实体与聚合体信息 (2)

Entity 1 polymer

聚合体 Polymer

来源 Source

Entity 2 non-polymer

7. 引用文献 (1)

8. 文件与曲线 (10)

Files (7)

Curves (3)